.

 where n is an integer specifying the number of different types of molecule appearing in the FIELD file. Once this directive has been encountered, DL_POLY_2 enters the molecular description environment in which only molecular decription keywords and data are valid.

Immediately following the molecules directive, are the records defining individual molecules:

1. name-of-molecule
   which can be any character string up to 80 characters in length. (Note: this is not a directive, just a simple character string.)
2. nummols n
   where n is the number of times a molecule of this type appears in the simulated system. The molecular data then follow in subsequent records:
3. atoms n
   where n indicates the number of atoms in this type of molecule. A number of records follow, each giving details of the atoms in the molecule i.e. site names, masses and charges. Each record carries the entries:

   
   		 sitnam 		 a8 		 atomic site name
   
   weight 		 real 		 atomic site mass
   
   chge 		 real 		 atomic site charge
   
   nrept 		 integer 		 repeat counter
   
   ifrz 		 integer 		 `frozen' atom (if ifrz$>0$)
   
   igrp 		 integer 		 neutral/charge group number
   
   
   

   The integer nrept need not be specified (in which case a value of 1 is assumed.) A number greater than 1 specified here indicates that the next (nrept - 1) entries in the CONFIG file are ascribed the atomic characteristics given in the current record. The sum of the repeat numbers for all atoms in a molecule should equal the number specified by the atoms directive.

4. shell n
   where n is the number of core-shell units. Each of the subsequent n records contains:

   
   		 index 1 		 integer 		 site index of core
   
   
   index 2 		 integer 		 site index of shell
   
   
   spring 		 real 		 force constant of core-shell spring
   
   
   

   The spring force constant is entered in units of engunit Å$^{-2}$, where engunit is the energy unit specified in the units directive.

   Note that the atomic site indices referred to in this table are indices arising from numbering each atom in the molecule from 1 to the number specified in the atoms directive for this molecule. This same numbering scheme should be used for all descriptions of this molecule, including the bonds, constraints, angles, and dihedrals entries described below. DL_POLY_2 will itself construct the global indices for all atoms in the systems.

   This directive (and associated data records) need not be specified if the molecule contains no core-shell units.

5. bonds n
   where n is the number of flexible chemical bonds in the molecule. Each of the subsequent n records contains:

   
   		 bond key 		 a4 		 see table 4.7
   
   
   index 1 		 integer 		 first atomic site in bond
   
   
   index 2 		 integer 		 second atomic site in bond
   
   
   variable 1 		 real 		 potential parameter see table 4.7
   
   
   variable 2 		 real 		 potential parameter see table 4.7
   
   
   variable 3 		 real 		 potential parameter see table 4.7
   
   
   variable 4 		 real 		 potential parameter see table 4.7
   
   
   

   The meaning of these variables is given in table 4.7. This directive (and associated data records) need not be specified if the molecule contains no flexible chemical bonds. See the note on the atomic indices appearing under the shell directive above.

   
   

   Table 4.7: Chemical bond potentials

   key	potential type	Variables (1-4)				functional form
   harm	Harmonic	$k$	$r_{0}$			$U(r)=\frac{1}{2}k(r-r_{0})^2$
   -hrm
   mors	Morse	$E_{0}$	$r_{0}$	$k$		$U(r)=E_{0}[\{1-\exp(-k(r-r_{0}))\}^{2}-1]$
   -mrs
   12-6	12-6	$A$	$B$			$U(r)=\left (\frac{A}{r^{12}}\right)-\left(\frac{B}{r^{6}}\right)$
   -126
   rhrm	Restraint	$k$	$r_{0}$	$r_{c}$		$U(r)=\frac{1}{2}k(r-r_{0})^2~~~~~~~~~\vert r-r_{0}\vert\le r_{c}$
   						$U(r)=\frac{1}{2}kr_{c}^2+kr_{c}(\vert r-r_{0}\vert-r_{c})~~~~\vert r-r_{0}\vert>r_{c}$
   -rhm
   quar	Quartic	$k$	$r_{0}$	$k'$	$k''$	$U(r)=\frac{k}{2}(r -r_{0})^2+\frac{k'}{3}(r-r_{0})^3+\frac{k''}{4}(r-r_{0})^4$
   -qur

   Note: bond potentials with a dash (-) as the first character of the keyword, do not contribute to the excluded atoms list (see section 2.1). In this case DL_POLY_2 will also calculate the nonbonded pair potentials between the described atoms, unless these are deactivated by another potential specification.

   
   

6. constraints n
   where n is the number of constraint bonds in the molecule. Each of the following n records contains:

   
   		 index 1 		 integer 		 first atomic index
   
   
   index 2 		 integer 		 second atomic index
   
   
   bondlength 		 real 		 constraint bond length
   
   
   

   This directive (and associated data records) need not be specified if the molecule contains no constraint bonds. See the note on the atomic indices appearing under the shell directive above.

7. pmf b
   where b is the potential of mean force bondlength (Å). There follows the definitions of two PMF units:
   1. pmf unit n$_{1}$
      where n$_{1}$ is the number of sites in the first unit. The subsequent n$_{1}$ records provide the site indices and weighting. Each record contains:

      
      		 index 		 integer 		 atomic site index
      
      
      weight 		 real 		 site weighting
      
      
      

   2. pmf unit n$_{2}$
      where n$_{2}$ is the number of sites in the second unit. The subsequent n$_{2}$ records provide the site indices and weighting. Each record contains:

      
      		 index 		 integer 		 atomic site index
      
      
      weight 		 real 		 site weighting
      
      
      

   This directive (and associated data records) need not be specified if no PMF constraints are present. See the note on the atomic indices appearing under the shell directive above. The pmf bondlength applies to the distance between the centres of the two pmf units. The centre, $\mbox{$\underline{R}$}$, of each unit is given by
   
   $$\mbox{$\underline{R}$} = {\sum_{\alpha} w_{\alpha} \mbox{$\underline{r}$}_{\alpha} \over \sum_{\alpha} w_{\alpha}}$$
   
   
   where $\mbox{$\underline{r}$}_{\alpha}$ is a site position and $w_{\alpha}$ the site weighting. Note that the pmf constraint is intramolecular. To define a constraint between two molecules, the molecules must be described as part of the same DL_POLY ``molecule''. This is illustrated in test case 6, where a pmf constraint is imposed between a potassium ion and the centre of mass of a water molecule. DL_POLY_2 allows only one type of pmf constraint per system. The value of nummols for this molecule determines the number of pmf constraint in the system.

   Note that the directive ensemble pmf must be specified in the CONTROL file for this option to be implemented correctly.

8. angles n
   where n is the number of valence angle bonds in the molecule. Each of the n records following contains:

   
   

   Table 4.8: Valence Angle potentials

   key	potential type	Variables (1-4)				functional form
   harm	Harmonic	$k$	$\theta_{0}$			$U(\theta)= {k\over 2} (\theta - \theta_0)^2$
   -hrm
   quar	Quartic	$k$	$\theta_{0}$	$k'$	$k''$	$U(\theta)= {k\over 2}(\theta - \theta_0)^2 + {k'\over 3}(\theta - \theta_0)^3 + {k''\over 4}(\theta - \theta_0)^4$
   -qur
   thrm	Truncated harmonic	$k$	$\theta_{0}$	$\rho$		$U(\theta)= {k\over 2} (\theta - \theta_0)^2 \exp[-(r_{ij}^8 + r_{ik}^8)/\rho^8]$
   -thm
   shrm	Screened harmonic	$k$	$\theta_{0}$	$\rho_{1}$	$\rho_{2}$	$U(\theta)= {k\over 2} (\theta - \theta_0)^2\exp[-(r_{ij}/\rho_1 + r_{ik}/\rho_2)]$
   -shm
   bvs1	Screened Vessal[24]	$k$	$\theta_{0}$	$\rho_{1}$	$\rho_{2}$	$U(\theta)= {k \over 8(\theta-\theta_0)^2}\left\{ \left[ (\theta_0 -\pi)^2 -(\theta-\pi)^2\right]^2\right\}$
   -bv1						$\exp[-(r_{ij}/\rho_1 + r_{ik}/\rho_2)]$
   bvs2	Truncated Vessal[25]	$k$	$\theta_{0}$	$a$	$\rho$	$U(\theta)= k\big[ \theta^a (\theta-\theta_0)^2 (\theta+\theta_0-2\pi)^2 - {a\over 2} \pi^{a-1}$
   -bv2						$(\theta-\theta_0)^2(\pi - \theta_0)^3\big] \exp[-(r_{ij}^8 + r_{ik}^8)/\rho^8]$
   hcos	Harmonic Cosine	$k$	$\theta_{0}$			$U(\theta)={k\over 2}(cos(\theta) -cos(\theta_{0}))^{2}$
   -hcs
   cos	Cosine	$A$	$\delta$	$m$		$U(\theta)=A[1+cos(m\theta-\delta)]$
   -cos
   $\theta$ is the a-b-c angle.

   Note: valence angle potentials with a dash (-) as the first character of the keyword, do not contribute to the excluded atoms list (see section 2.1). In this case DL_POLY_2 will calculate the nonbonded pair potentials between the described atoms.

   
   

   
   		 angle key 		 a4 		 potential key. See table 4.8
   
   
   index 1 		 integer 		 first atomic index
   
   
   index 2 		 integer 		 second atomic index (central site)
   
   
   index 3 		 integer 		 third atomic index
   
   
   variable 1 		 real 		 potential parameter see table4.8
   
   
   variable 2 		 real 		 potential parameter see table4.8
   
   
   

   The meaning of these variables is given in table 4.8. See the note on the atomic indices appearing under the shell directive above. This directive (and associated data records) need not be specified if the molecule contains no angular terms.
9. dihedrals n
   where n is the number of dihedral interactions present in the molecule. Each of the following n records contains:

   
   		 dihedral key 		 a4 		 potential key. See table 4.9
   
   
   index 1 		 integer 		 first atomic index
   
   
   index 2 		 integer 		 second atomic index
   
   
   index 3 		 integer 		 third atomic index
   
   
   index 4 		 integer 		 fourth atomic index
   
   
   variable 1 		 real 		 potential parameter see table4.9
   
   
   variable 2 		 real 		 potential parameter see table4.9
   
   
   variable 3 		 real 		 potential parameter see table4.9
   
   
   variable 4 		 real 		 1-4 electrostatic interaction scale factor.
   
   
   variable 5 		 real 		 1-4 Van der Waals interaction scale factor.
   
   
   

   The meaning of the variables 1-3 is given in table 4.9. The variables 4 and 5 specify the scaling factor for the 1-4 electrostatic and Van der Waals nonbonded interactions respectively. This directive (and associated data records) need not be specified if the molecule contains no dihedral angle terms. See the note on the atomic indices appearing under the shell directive above.

   
   

   Table 4.9: Dihedral Angle Potentials

   key	potential type	Variables (1-3)			functional form
   cos	Cosine	$A$	$\delta$	$m$	$U(\phi)= A \left [ 1 + \cos (m\phi - \delta)\right]$
   harm	Harmonic	$k$	$\phi_0$		$U(\phi)= {1\over 2} k (\phi - \phi_0)^2$
   hcos	Harmonic cosine	$k$	$\phi_{0}$		$U(\phi)={k\over 2}(cos(\phi) -cos(\phi_{0}))^{2}$
   cos3	Triple cosine	$A_{1}$	$A_{2}$	$A_{3}$	$U(\phi)= {1\over 2}A_{1}(1+cos(\phi))+{1\over 2}A_{2}(1-cos(2\phi))$
   					$+{1\over 2}A_{3}(1+cos(3\phi))$
   $\phi$ is the a-b-c-d dihedral angle.
   
   

10. inversions n
    where n is the number of inversion interactions present in the molecule. Each of the following n records contains:

    
    		 inversion key 		 a4 		 potential key. See table 4.10
    
    
    index 1 		 integer 		 first atomic index
    
    
    index 2 		 integer 		 second atomic index
    
    
    index 3 		 integer 		 third atomic index
    
    
    index 4 		 integer 		 fourth atomic index
    
    
    variable 1 		 real 		 potential parameter see table4.10
    
    
    variable 2 		 real 		 potential parameter see table4.10
    
    
    

    The meaning of the variables 1-2 is given in table 4.10. This directive (and associated data records) need not be specified if the molecule contains no inversion angle terms. See the note on the atomic indices appearing under the shell directive above.

    
    

    Table 4.10: Inversion Angle Potentials

    key	potential type	Variables (1-2)		functional form
    harm	Harmonic	$k$	$\phi_0$	$U(\phi)= {1\over 2} k (\phi - \phi_0)^2$
    hcos	Harmonic cosine	$k$	$\phi_{0}$	$U(\phi)={k\over 2}(cos(\phi) -cos(\phi_{0}))^{2}$
    plan	Planar	$A$		$U(\phi)= A \left [ 1 - \cos (\phi)\right]$
    $\phi$ is the inversion angle.
    
    

11. rigid n
    where n is the number of rigid units in the molecule. It is followed by at least n records, each specifying the sites in a rigid unit:

    
    		 m 		 integer 		 number of sites in rigid unit
    
    
    site 1 		 integer 		 first site atomic index
    
    
    site 2 		 integer 		 second site atomic  index
    
    
    site 3 		 integer 		 third site atomic index
    
    .. 		 .. 		 etc.
    
    
    site m 		 integer 		 m'th site atomic index
    
    
    

    Up to 15 sites can be specified on the first record. Additional records are used if necessary. Up to 16 sites are specified per record thereafter.

    This directive (and associated data records) need not be specified if the molecule contains no rigid units. See the note on the atomic indices appearing under the shell directive above.

12. teth n
    where n is the number of tethered atoms in the molecule. It is followed by n records specifying the tethered sites in the molecule:

    
    		 tether key 		 a4 		 tethering potential key  see table 4.11
    
    
    index 		 integer 		 atomic index 
    
    
    variable 1 		 real 		 potential parameter see table4.11
    
    
    variable 2 		 real 		 potential parameter see table4.11
    
    
    variable 3 		 real 		 potential parameter see table4.11
    
    
    variable 4 		 real 		 potential parameter see table4.11
    
    
    

    This directive (and associated data records) need not be specified if the molecule contains no tethered atoms. See the note on the atomic indices appearing under the shell directive above.

    
    

    Table 4.11: Tethering potentials

    key	potential type	Variables (1-3)			functional form
    harm	Harmonic	$k$			$U(r)=\frac{1}{2}kr^2$
    rhrm	Restraint	$k$	$r_{c}$		$U(r)=\frac{1}{2}kr^2~~~~~~r \le r_{c}$
    					$U=\frac{1}{2}kr_{c}^2+kr_{c}(r-r_{c})~~~~~~r>r_{c}$
    quar	Quartic	$k$	$k'$	$k''$	$U(r)=\frac{k}{2}r^2+ \frac{k'}{3}r^3+\frac{k''}{4}r^4$

    
    

13. finish
    This directive is entered to signal to DL_POLY_2 that the entry of the details of a molecule has been completed.

    The entries for a second molecule may now be entered, beginning with the name-of-molecule record and ending with the finish directive.

    The cycle is repeated until all the types of molecules indicated by the molecules directive have been entered.

The user is recommended to look at the example FIELD files in the data directory to see how typical FIELD files are constructed.